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Default parameters for generation of synthetic single cell data (RNA)

params_sc_synthetic_data.Rd

For the generation of synthetic single cell data mostly for testing or showcasing purposes. The default configurations generates 1000 cells x 100 genes with genes 1:10 being cell markers for cell type 1, genes 11:20 for cell type 2 and genes 21:30 for cell type.

Usage

params_sc_synthetic_data(
  n_cells = 1000L,
  n_genes = 100L,
  n_batches = 1L,
  marker_genes = list(cell_type_1 = list(marker_genes = 0:9), cell_type_2 =
    list(marker_genes = 10:19), cell_type_3 = list(marker_genes = 20:29)),
  batch_effect_strength = c("strong", "medium", "weak"),
  n_samples = NULL,
  sample_bias = NULL
)

Arguments

n_cells

Integer. Number of cells. Defaults to 1000L.

n_genes

Integer. Number of genes. Defaults to 100L.

n_batches

Integer. Number of batches. Defaults to 1L.

marker_genes

Any. A nested list that indicates which gene indices are markers for which cell. Defaults to list(cell_type_1 = list(marker_genes = 0:9), cell_type_2 = list(marker_genes = 10:19), cell_type_3 = list(marker_genes = 20:29)).

batch_effect_strength

String. The strength of the batch effect to add. One of c("strong", "medium", "weak"). Defaults to "strong".

n_samples

Integer or NULL. Shall sample membership be added to the synthetic data. If you want sample information you need to provide n_samples and sample_bias. Defaults to NULL.

sample_bias

Any. One of c("even", "slightly_uneven", "very_uneven") Defaults to NULL.

Value

A named list with the following elements:

  • n_cells - Integer. Number of cells. Defaults to 1000L.

  • n_genes - Integer. Number of genes. Defaults to 100L.

  • marker_genes - Any. A nested list that indicates which gene indices are markers for which cell. Defaults to list(cell_type_1 = list(marker_genes = 0:9), cell_type_2 = list(marker_genes = 10:19), cell_type_3 = list(marker_genes = 20:29)).

  • n_batches - Integer. Number of batches. Defaults to 1L.

  • batch_effect_strength - String. The strength of the batch effect to add. One of c("strong", "medium", "weak"). Defaults to "strong".

  • n_samples - Integer or NULL. Shall sample membership be added to the synthetic data. If you want sample information you need to provide n_samples and sample_bias. Defaults to NULL.

  • sample_bias - Any. One of c("even", "slightly_uneven", "very_uneven") Defaults to NULL.